Hi, Pressure can often fluctuate wildly, especially in relatively small systems. You probably won't be able to achieve a stable pressure of 1 atm, and that's not a problem. As long as your pressure fluctuates around 1 atm you should be fine (you can use running average in xmgrace to check for this out). If it's not close enough yet, try extending your NPT equilibration until you are satisfied. The density is often a more stable indicator.
Kind regards Dries On 10 May 2017 at 12:25, Quin K <profiles...@gmail.com> wrote: > Hi > > I used lyzozyme in water tutorial by virginia tech for MD simulation of a > protein, *pdb id = 2NT7*. > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx > -tutorials/lysozyme/index.html > During equilibration step of MD simulation for a protein I got following > results for pressure. > Would the minus pressure value be a problem during MD production step? > What should be done to increase the pressure to 1 atm ? > > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------ > ------------------- > Pressure -1.83425 2.8 124.812 -0.905452 (bar) > > > > *Other results:* > > Energy Average Err.Est. RMSD Tot-Drift > ------------------------------------------------------------ > ------------------- > Density 1025.74 0.32 2.01623 1.97406 > (kg/m^3) > > > > Thanks > Regards > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
